Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate CCNA_00424 CCNA_00424 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Caulo:CCNA_00424 Length = 479 Score = 288 bits (737), Expect = 3e-82 Identities = 173/475 (36%), Positives = 263/475 (55%), Gaps = 16/475 (3%) Query: 21 TGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDP 80 T +I+ +V + T ++P+TEE + D+D AV AA AF +S+S + Sbjct: 5 TKFYIDGAWVDPAAPNTLDVINPATEEVCGVISMGSEADVDKAVRAARKAF-ASFSQTSR 63 Query: 81 QVRMKVLYKLADLIDEHADTLAHIEALDNGK-SLMCSKGDVALTAAYFRSCAGWTDKIKG 139 + R+ +L ++ + + +A + G + + + A+ + ++ A +KG Sbjct: 64 EERIDILERIIAEYQKRFEDMAKAITEEMGAPAWLAQRAQAAMGIGHVQTAAA---VLKG 120 Query: 140 SVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSA 199 E D +EPIGVC I PWN+P+ + K+GP + TGCT VLK +E P S Sbjct: 121 YKFEE-DRGTTRIVKEPIGVCAFITPWNWPVNQIACKVGPAIATGCTMVLKPSEIAPFSG 179 Query: 200 LYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESN 259 ++ AG P GV N+V+G GPT GA +S HP++ V+FTGST G + K AA + Sbjct: 180 YIWTEIMHAAGVPAGVFNLVNGDGPTVGAALSRHPEVDMVSFTGSTRAGIEVAKNAAPT- 238 Query: 260 LKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSE 319 +K+V ELGGKSPNI+ DDAD + V + N+G+ C A +R+ V D++++ Sbjct: 239 VKRVHQELGGKSPNIILDDADFSRAVAGGVASVMMNSGQSCNAPTRMLVPGARMDEVIAI 298 Query: 320 FKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG---ERFGNKG 376 K AAES +GDP + MG S+ Q +KI I G EGAT++TGG +KG Sbjct: 299 AKAAAESHTVGDP-NGNHKMGPVVSETQWNKIQGLIQKGIDEGATLVTGGVGRPEGLDKG 357 Query: 377 YFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLST 436 Y++KPT+F +V + I ++EIFGPVV+I + TV+E + + ND+EYGLAA V + Sbjct: 358 YYVKPTVFANVTNEMTIAKEEIFGPVVSILGYDTVDEAVTVGNDTEYGLAAYVSGGDQDE 417 Query: 437 AISVSNKINSGTIWVNTYNDFHP--MVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 V++++ +G + T N P M PFGGY SG GRE G+ A + + KA+ Sbjct: 418 VRKVASRLRAGQV---TLNGAGPDLMAPFGGYKMSGNGREWGDHAFGEFLETKAI 469 Lambda K H 0.316 0.133 0.389 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 610 Number of extensions: 34 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 495 Length of database: 479 Length adjustment: 34 Effective length of query: 461 Effective length of database: 445 Effective search space: 205145 Effective search space used: 205145 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory